Chao Chen

Saumya Gupta, Xiaoling Hu, James Kaan et al.

Deep learning methods have achieved impressive performance for multi-class medical image segmentation. However, they are limited in their ability to encode topological interactions among different classes (e.g., containment and exclusion). These constraints naturally arise in biomedical images and can be crucial in improving segmentation quality. In this paper, we introduce a novel topological interaction module to encode the topological interactions into a deep neural network. The implementation is completely convolution-based and thus can be very efficient. This empowers us to incorporate the constraints into end-to-end training and enrich the feature representation of neural networks. The efficacy of the proposed method is validated on different types of interactions. We also demonstrate the generalizability of the method on both proprietary and public challenge datasets, in both 2D and 3D settings, as well as across different modalities such as CT and Ultrasound. Code is available at: https://github.com/TopoXLab/TopoInteraction

Wenjia Zhang, Yikai Zhang, Xiaoling Hu et al.

The adversarial risk of a machine learning model has been widely studied. Most previous works assume that the data lies in the whole ambient space. We propose to take a new angle and take the manifold assumption into consideration. Assuming data lies in a manifold, we investigate two new types of adversarial risk, the normal adversarial risk due to perturbation along normal direction, and the in-manifold adversarial risk due to perturbation within the manifold. We prove that the classic adversarial risk can be bounded from both sides using the normal and in-manifold adversarial risks. We also show with a surprisingly pessimistic case that the standard adversarial risk can be nonzero even when both normal and in-manifold risks are zero. We finalize the paper with empirical studies supporting our theoretical results. Our results suggest the possibility of improving the robustness of a classifier by only focusing on the normal adversarial risk.

Xiaoling Hu, Dimitris Samaras, Chao Chen

Accurate delineation of fine-scale structures is a very important yet challenging problem. Existing methods use topological information as an additional training loss, but are ultimately making pixel-wise predictions. In this paper, we propose the first deep learning based method to learn topological/structural representations. We use discrete Morse theory and persistent homology to construct an one-parameter family of structures as the topological/structural representation space. Furthermore, we learn a probabilistic model that can perform inference tasks in such a topological/structural representation space. Our method generates true structures rather than pixel-maps, leading to better topological integrity in automatic segmentation tasks. It also facilitates semi-automatic interactive annotation/proofreading via the sampling of structures and structure-aware uncertainty.

Chen Li, Xiaoling Hu, Shahira Abousamra et al.

Generative models, such as GANs and diffusion models, have been used to augment training sets and boost performances in different tasks. We focus on generative models for cell detection instead, i.e., locating and classifying cells in given pathology images. One important information that has been largely overlooked is the spatial patterns of the cells. In this paper, we propose a spatial-pattern-guided generative model for cell layout generation. Specifically, a novel diffusion model guided by spatial features and generates realistic cell layouts has been proposed. We explore different density models as spatial features for the diffusion model. In downstream tasks, we show that the generated cell layouts can be used to guide the generation of high-quality pathology images. Augmenting with these images can significantly boost the performance of SOTA cell detection methods. The code is available at https://github.com/superlc1995/Diffusion-cell.

Chao Chen, Haoyu Geng, Gang Zeng et al.

Inductive one-bit matrix completion is motivated by modern applications such as recommender systems, where new users would appear at test stage with the ratings consisting of only ones and no zeros. We propose a unified graph signal sampling framework which enjoys the benefits of graph signal analysis and processing. The key idea is to transform each user's ratings on the items to a function (signal) on the vertices of an item-item graph, then learn structural graph properties to recover the function from its values on certain vertices -- the problem of graph signal sampling. We propose a class of regularization functionals that takes into account discrete random label noise in the graph vertex domain, then develop the GS-IMC approach which biases the reconstruction towards functions that vary little between adjacent vertices for noise reduction. Theoretical result shows that accurate reconstructions can be achieved under mild conditions. For the online setting, we develop a Bayesian extension, i.e., BGS-IMC which considers continuous random Gaussian noise in the graph Fourier domain and builds upon a prediction-correction update algorithm to obtain the unbiased and minimum-variance reconstruction. Both GS-IMC and BGS-IMC have closed-form solutions and thus are highly scalable in large data. Experiments show that our methods achieve state-of-the-art performance on public benchmarks.

Yikai Zhang, Jiachen Yao, Yusu Wang et al.

Topological loss based on persistent homology has shown promise in various applications. A topological loss enforces the model to achieve certain desired topological property. Despite its empirical success, less is known about the optimization behavior of the loss. In fact, the topological loss involves combinatorial configurations that may oscillate during optimization. In this paper, we introduce a general purpose regularized topology-aware loss. We propose a novel regularization term and also modify existing topological loss. These contributions lead to a new loss function that not only enforces the model to have desired topological behavior, but also achieves satisfying convergence behavior. Our main theoretical result guarantees that the loss can be optimized efficiently, under mild assumptions.

Zuoyu Yan, Tengfei Ma, Liangcai Gao et al.

Cycles are fundamental elements in graph-structured data and have demonstrated their effectiveness in enhancing graph learning models. To encode such information into a graph learning framework, prior works often extract a summary quantity, ranging from the number of cycles to the more sophisticated persistence diagram summaries. However, more detailed information, such as which edges are encoded in a cycle, has not yet been used in graph neural networks. In this paper, we make one step towards addressing this gap, and propose a structure encoding module, called CycleNet, that encodes cycle information via edge structure encoding in a permutation invariant manner. To efficiently encode the space of all cycles, we start with a cycle basis (i.e., a minimal set of cycles generating the cycle space) which we compute via the kernel of the 1-dimensional Hodge Laplacian of the input graph. To guarantee the encoding is invariant w.r.t. the choice of cycle basis, we encode the cycle information via the orthogonal projector of the cycle basis, which is inspired by BasisNet proposed by Lim et al. We also develop a more efficient variant which however requires that the input graph has a unique shortest cycle basis. To demonstrate the effectiveness of the proposed module, we provide some theoretical understandings of its expressive power. Moreover, we show via a range of experiments that networks enhanced by our CycleNet module perform better in various benchmarks compared to several existing SOTA models.

Ziqing Ma, Wenwei Wang, Tian Zhou et al.

Accurate solar power forecasting is crucial to integrate photovoltaic plants into the electric grid, schedule and secure the power grid safety. This problem becomes more demanding for those newly installed solar plants which lack sufficient data. Current research predominantly relies on historical solar power data or numerical weather prediction in a single-modality format, ignoring the complementary information provided in different modalities. In this paper, we propose a multi-modality fusion framework to integrate historical power data, numerical weather prediction, and satellite images, significantly improving forecast performance. We introduce a vector quantized framework that aligns modalities with varying information densities, striking a balance between integrating sufficient information and averting model overfitting. Our framework demonstrates strong zero-shot forecasting capability, which is especially useful for those newly installed plants. Moreover, we collect and release a multi-modal solar power (MMSP) dataset from real-world plants to further promote the research of multi-modal solar forecasting algorithms. Our extensive experiments show that our model not only operates with robustness but also boosts accuracy in both zero-shot forecasting and scenarios rich with training data, surpassing leading models. We have incorporated it into our eForecaster platform and deployed it for more than 300 solar plants with a capacity of over 15GW.

Xize Liang, Chao Chen, Shuang Qiu et al.

Preference alignment is pivotal for empowering large language models (LLMs) to generate helpful and harmless responses. However, the performance of preference alignment is highly sensitive to the prevalent noise in the preference data. Recent efforts for this problem either marginally alleviate the impact of noise without the ability to actually reduce its presence, or rely on costly teacher LLMs prone to reward misgeneralization. To address these challenges, we propose the RObust Preference Optimization (ROPO) framework, an iterative alignment approach that integrates noise-tolerance and filtering of noisy samples without the aid of external models. Specifically, ROPO iteratively solves a constrained optimization problem, where we dynamically assign a quality-aware weight for each sample and constrain the sum of the weights to the number of samples we intend to retain. For noise-tolerant training and effective noise identification, we derive a robust loss by suppressing the gradients of samples with high uncertainty. We demonstrate both empirically and theoretically that the derived loss is critical for distinguishing noisy samples from clean ones. Furthermore, inspired by our derived loss, we propose a robustness-guided rejection sampling technique to compensate for the potential important information in discarded queries. Experiments on three widely-used datasets with Mistral-7B and Llama-2-7B demonstrate that ROPO significantly outperforms existing preference alignment methods, with its superiority growing as the noise rate increases.

Rui Xu, Chao Chen, Yue Sun et al.

Conformal prediction yields a prediction set with guaranteed $1-α$ coverage of the true target under the i.i.d. assumption, which may not hold and lead to a gap between $1-α$ and the actual coverage. Prior studies bound the gap using total variation distance, which cannot identify the gap changes under distribution shift at a given $α$. Besides, existing methods are mostly limited to covariate shift,while general joint distribution shifts are more common in practice but less researched.In response, we first propose a Wasserstein distance-based upper bound of the coverage gap and analyze the bound using probability measure pushforwards between the shifted joint data and conformal score distributions, enabling a separation of the effect of covariate and concept shifts over the coverage gap. We exploit the separation to design an algorithm based on importance weighting and regularized representation learning (WR-CP) to reduce the Wasserstein bound with a finite-sample error bound.WR-CP achieves a controllable balance between conformal prediction accuracy and efficiency. Experiments on six datasets prove that WR-CP can reduce coverage gaps to $3.2\%$ across different confidence levels and outputs prediction sets 37$\%$ smaller than the worst-case approach on average.

Rui Xu, Yue Sun, Chao Chen et al.

Uncertainty is critical to reliable decision-making with machine learning. Conformal prediction (CP) handles uncertainty by predicting a set on a test input, hoping the set to cover the true label with at least $(1-α)$ confidence. This coverage can be guaranteed on test data even if the marginal distributions $P_X$ differ between calibration and test datasets. However, as it is common in practice, when the conditional distribution $P_{Y|X}$ is different on calibration and test data, the coverage is not guaranteed and it is essential to measure and minimize the coverage loss under distributional shift at \textit{all} possible confidence levels. To address these issues, we upper bound the coverage difference at all levels using the cumulative density functions of calibration and test conformal scores and Wasserstein distance. Inspired by the invariance of physics across data distributions, we propose a physics-informed structural causal model (PI-SCM) to reduce the upper bound. We validated that PI-SCM can improve coverage robustness along confidence level and test domain on a traffic speed prediction task and an epidemic spread task with multiple real-world datasets.

Zuoyu Yan, Tengfei Ma, Liangcai Gao et al.

Topological features based on persistent homology capture high-order structural information so as to augment graph neural network methods. However, computing extended persistent homology summaries remains slow for large and dense graphs and can be a serious bottleneck for the learning pipeline. Inspired by recent success in neural algorithmic reasoning, we propose a novel graph neural network to estimate extended persistence diagrams (EPDs) on graphs efficiently. Our model is built on algorithmic insights, and benefits from better supervision and closer alignment with the EPD computation algorithm. We validate our method with convincing empirical results on approximating EPDs and downstream graph representation learning tasks. Our method is also efficient; on large and dense graphs, we accelerate the computation by nearly 100 times.

Zuoyu Yan, Tengfei Ma, Liangcai Gao et al.

In recent years, algebraic topology and its modern development, the theory of persistent homology, has shown great potential in graph representation learning. In this paper, based on the mathematics of algebraic topology, we propose a novel solution for inductive relation prediction, an important learning task for knowledge graph completion. To predict the relation between two entities, one can use the existence of rules, namely a sequence of relations. Previous works view rules as paths and primarily focus on the searching of paths between entities. The space of rules is huge, and one has to sacrifice either efficiency or accuracy. In this paper, we consider rules as cycles and show that the space of cycles has a unique structure based on the mathematics of algebraic topology. By exploring the linear structure of the cycle space, we can improve the searching efficiency of rules. We propose to collect cycle bases that span the space of cycles. We build a novel GNN framework on the collected cycles to learn the representations of cycles, and to predict the existence/non-existence of a relation. Our method achieves state-of-the-art performance on benchmarks.

Shahira Abousamra, Minh Hoai, Dimitris Samaras et al.

We address the problem of crowd localization, i.e., the prediction of dots corresponding to people in a crowded scene. Due to various challenges, a localization method is prone to spatial semantic errors, i.e., predicting multiple dots within a same person or collapsing multiple dots in a cluttered region. We propose a topological approach targeting these semantic errors. We introduce a topological constraint that teaches the model to reason about the spatial arrangement of dots. To enforce this constraint, we define a persistence loss based on the theory of persistent homology. The loss compares the topographic landscape of the likelihood map and the topology of the ground truth. Topological reasoning improves the quality of the localization algorithm especially near cluttered regions. On multiple public benchmarks, our method outperforms previous localization methods. Additionally, we demonstrate the potential of our method in improving the performance in the crowd counting task.

Xiaoling Hu, Li Fuxin, Dimitris Samaras et al.

Segmentation algorithms are prone to make topological errors on fine-scale structures, e.g., broken connections. We propose a novel method that learns to segment with correct topology. In particular, we design a continuous-valued loss function that enforces a segmentation to have the same topology as the ground truth, i.e., having the same Betti number. The proposed topology-preserving loss function is differentiable and we incorporate it into end-to-end training of a deep neural network. Our method achieves much better performance on the Betti number error, which directly accounts for the topological correctness. It also performs superiorly on other topology-relevant metrics, e.g., the Adjusted Rand Index and the Variation of Information. We illustrate the effectiveness of the proposed method on a broad spectrum of natural and biomedical datasets.

Chao Chen, Xiaoqing Zhu, Gustavo de Veciana et al.

Adapting video data rate during streaming can effectively reduce the risk of playback interruptions caused by channel throughput fluctuations. The variations in rate, however, also introduce video quality fluctuations and thus potentially affects viewers' Quality of Experience (QoE). We show how the QoE of video users can be improved by rate adaptation and admission control. We conducted a subjective study wherein we found that viewers' QoE was strongly correlated with the empirical cumulative distribution function (eCDF) of the predicted video quality. Based on this observation, we propose a rate-adaptation algorithm that can incorporate QoE constraints on the empirical cumulative quality distribution per user. We then propose a threshold-based admission control policy to block users whose empirical cumulative quality distribution is not likely to satisfy their QoE constraint. We further devise an online adaptation algorithm to automatically optimize the threshold. Extensive simulation results show that the proposed scheme can reduce network resource consumption by $40\%$ over conventional average-quality maximized rate-adaptation algorithms.